From all accounts, it seems as if the Escherichia, Enterobacter, etc. that live and thrive in the human gut are pretty well entrenched. I know that these microbial populations are often analyzed as an ecosystem.

What surprises me is that it seems like minor food poisoning can throw the whole ecosystem off. I know superficially that Clostridium are contenders in the fight because they remain viable after traveling through the acid of the stomach, but why are these populations so sensitive to other invading bacteria?

Hi! Could you please give some references to the fact that minor food poisoning can throw the whole ecosystem off? This is very interesting to me, as a personal health matter.
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dsignJan 5 '12 at 7:59

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@dignor.sign I was more making an observation, but see en.wikipedia.org/wiki/Gut_flora#Alterations_in_flora_balance, A reduction in levels of native bacterial species also disrupts their ability to inhibit the growth of harmful species. They cite 3 references, including a Lancet article, but say that this may in fact not be the cause of symptoms such as diarrhea (apologies for the graphic description).
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jonscaJan 5 '12 at 12:24

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I was just curious about how weak this ecosystem can be; these papers will do it. Thanks!
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dsignJan 5 '12 at 17:02

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Keep in mind one of the most common harmful species is a native species in many people: Clostridium difficile.
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FomiteJan 10 '12 at 23:04

@EpiGrad Excellent point. If your up for it, elaborate it a bit as an answer. I don't know much about how it achieves balance with E. coli.
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jonscaJan 10 '12 at 23:07

2 Answers
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This is the case when you consume food which is contaminated with some toxins, and those are responsible for development of the poisoning symptoms. The source organisms of these toxins might not be present anymore (killed by heating during cooking, for example). In this case there is no massive invasion of any foreign organisms into the gut.

Alimentary toxico-infection

This happens if you eat the food contaminated with microorganisms, and these start to massively proliferate in your alimentary system causing the symptoms of poisoning. The massive intake of the bacteria (even 2-3 spoons of contaminated food might contain millions of bacteria, like Staphilococcus in contaminated diary products). In this case the balance of gut microflora is dramatically changed due to introduction of a considerable amount of foreign microorganisms.

So, even the poisoning seems to be "minor" (e.g., its symptoms are not so dramatic), there could be different amounts of bacteria invading the guts.

The second important point here is the increased emptying of the gut due to diarrhea that leads to the washing out some of the "good" bacteria from the guts, especially in case of profuse diarrhea. The newly coming bacteria are not necessarily those that are present in normal microflora, and it takes days or even weeks until the microflora reaches homeostasis again.

One last point: even without poisoning, microflora varies, and the amount of different bacterial fractions can fluctuate over time. This is normal and depends upon your eating habits, your environment, immune status, and many other factors.

"Alterations to gut microflora" need not only be the invasion of a different, aggressive species of bacteria. One of the most common, and most dramatic forms of alteration to our gut flora is something we do to ourselves: antibiotics. Most ecosystems, micro or macro, are pretty vulnerable to the equivalent of a sustained firebombing.

Some of the "harmful bacteria" that benefit from a disruption of the gut microflora are constituent components of said flora. Clostridium difficile is part of the normal flora of many people - and acquired by many more transiently without incident - yet when the environment is sufficiently disrupted by antibiotics, peptic acid suppressors or some other factors, it proliferates and causes illness.

While it may feel awful to you, many GI illnesses are really just a transient invasion before the body clears the infection, and are only marginally disruptive, or not disruptive at all. This can include the intake of toxins without the actual organism, or things like norovirus, which has a low enough infectious dose that even small amounts will make you ill.